Table 1.

Comparison of traditional RNA-seq, SLAM-seq, and scRNA-seq. The below sequencing technologies have advantages and disadvantages; selecting the right approach depends on the experimental setup.

Technique	Description	Advantages	Limitations
Standard RNA-seq	Quantifies the levels of RNA from a biological sample at a given moment.	Not limited to known genes [9]. Enables analysis of alternative splicing.	Large amount of starting material needed (for typical library-preparation). Masks sample heterogeneity (for example in the case of biopsy [10]).
Nascent RNA-seq	Nucleotide analogue based techniques used to assess RNA synthesis. The nascent RNAs incorporate the nucleotide analogue and are either enriched using affinity-based techniques or decoded computationally.	Measures active transcription. Direct causality between regulator and target. Allows evaluation of mRNA half-lives and of mRNA degradation.	Laborious compared to RNA-seq. Selecting appropriate labeling time is critical: if too short, fails to provide a snapshot of mRNA synthesis; if too long, nascent and total-RNA cannot be distinguished.
scRNA-seq	Measures the gene expression levels at single cell resolution.	Allows assessment of the sample heterogeneity. Enables tracking (potential) cell-fate transitions/developmental steps.	Laborious compared to RNA-seq. Getting the cells to a single cell solution is challenging and choosing the right technique to do this is crucial.